rs1057560

Variant names:

• chr4-146256189-G-A
• rs1057560
• NM_001029998.6:c.*302C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029998.6(SLC10A7):​c.*302C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 408,904 control chromosomes in the GnomAD database, including 35,965 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.35 (11272 hom., cov: 33)
  • Exomes 𝑓: 0.43 (24693 hom.)
• Consequence: SLC10A7 NM_001029998.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 17 publications found

Genes affected

SLC10A7 (HGNC:23088): (solute carrier family 10 member 7) Enables bile acid transmembrane transporter activity. Involved in several processes, including cellular calcium ion homeostasis; glycoprotein transport; and heparin biosynthetic process. Located in Golgi apparatus and endoplasmic reticulum. Is intrinsic component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC10A7 Gene-Disease associations (from GenCC):

• short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001029998.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC10A7	NM_001029998.6	MANE Select	c.*302C>T		3_prime_UTR	Exon 12 of 12	NP_001025169.1	Q0GE19-2
	SLC10A7	NM_001300842.3		c.*359C>T		3_prime_UTR	Exon 13 of 13	NP_001287771.1	Q0GE19-1
	SLC10A7	NM_001317816.2		c.*302C>T		3_prime_UTR	Exon 11 of 11	NP_001304745.1	Q0GE19-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC10A7	ENST00000335472.12	TSL:1 MANE Select	c.*302C>T		3_prime_UTR	Exon 12 of 12	ENSP00000334594.8	Q0GE19-2
	SLC10A7	ENST00000432059.6	TSL:1	c.*302C>T		3_prime_UTR	Exon 11 of 11	ENSP00000411297.2	Q0GE19-3
	SLC10A7	ENST00000693222.1		c.*302C>T		3_prime_UTR	Exon 13 of 13	ENSP00000508969.1	A0A8I5QJB5

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53606 AN: 151986 Hom.: 11272 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.427 AC: 109661 AN: 256800 Hom.: 24693 Cov.: 0 AF XY: 0.427 AC XY: 58223 AN XY: 136242

African (AFR) AF: 0.100 AC: 736 AN: 7362

American (AMR) AF: 0.397 AC: 3786 AN: 9540

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 2887 AN: 7960

East Asian (EAS) AF: 0.285 AC: 4247 AN: 14914

South Asian (SAS) AF: 0.402 AC: 12994 AN: 32338

European-Finnish (FIN) AF: 0.431 AC: 6024 AN: 13968

Middle Eastern (MID) AF: 0.370 AC: 411 AN: 1110

European-Non Finnish (NFE) AF: 0.468 AC: 72482 AN: 154926

Other (OTH) AF: 0.415 AC: 6094 AN: 14682

GnomAD4 genome AF: 0.353 AC: 53618 AN: 152104 Hom.: 11272 Cov.: 33 AF XY: 0.352 AC XY: 26201 AN XY: 74358

African (AFR) AF: 0.108 AC: 4488 AN: 41548

American (AMR) AF: 0.404 AC: 6177 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1267 AN: 3464

East Asian (EAS) AF: 0.326 AC: 1688 AN: 5174

South Asian (SAS) AF: 0.406 AC: 1960 AN: 4822

European-Finnish (FIN) AF: 0.434 AC: 4582 AN: 10554

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32108 AN: 67942

Other (OTH) AF: 0.346 AC: 731 AN: 2110

Alfa AF: 0.427 Hom.: 28597

Bravo AF: 0.338

Asia WGS AF: 0.375 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1057560; hg19: chr4-147177341; COSMIC: COSV53888575; COSMIC: COSV53888575;